Fruit waste containing citrus fractions with high limonene content presents a particular challenge for anaerobic digestion (AD) due to the inhibitory effects of this terpene on methanogenic microorganisms. This study evaluates the performance of a pilot-scale biofilm anaerobic reactor treating mixed fruit waste with varying proportions of citrus residues, focusing on biogas production, methane composition, and process stability. A 1,167 L fiberglass reactor equipped with K1 biofilm carriers was operated under mesophilic conditions and fed with six different substrate formulations. The results indicate that increasing the proportion of citrus waste leads to reduced biogas production during the initial phase, accompanied by volatile fatty acid (VFA) accumulation and pH suppression, suggesting process inhibition driven by limonene. In contrast, formulations with moderated citrus content showed improved operational stability, characterized by pH values of 6.8–7.1, VFA/alkalinity ratios below 0.30, and higher methane fractions. Energy conversion analysis revealed that treatments with controlled limonene levels yielded the highest net energy output, while excessive citrus content decreased conversion efficiency. Correlation analysis confirmed strong associations between VFA accumulation, pH decline, and reduced methane concentration under high-limonene conditions. These findings demonstrate that managing the proportion of citrus-rich fruit waste is essential for maintaining process stability and enhancing biogas productivity in pilot-scale biofilm AD systems.